Hi, I have a situation with one of my customers that I am not sure how to approach and what to do, has anyone been in this situation before and if you did what did you do?

Business Case:

I made a sales order S02813 which has 1 product on it and a shipping charge 

product has Washoe County taxes on it and it's priced at 16.06 so taxes are 1.19 

The shipping charge is set to tax-exempt, and it's priced at 65 Placing our sales order total at 79.45 tax excluded and with taxes that 80.64 

I then made a down payment invoice for 100% and the system automatically made just 1 line for a full total of 79.45 and it applied to Washoe County because of the 1st item and the amount is the sum of the item price and shipping so taxes on the invoice is 6.57 totaling the invoice at 86.02 which is inaccurate because shipping shouldn't be included in the tax calculation on the invoice and taxes should be 1.19 like on the sales order?